In 1997, athenahealth cofounders Jonathan Bush and Todd Park started Athena Women's Health, a women's health and birthing practice in San Diego, California. Despite a booming business, the practice quickly encountered problems being reimbursed by payers. . Lacking a system to track insurance claims, Bush and Park formed athenahealth, Inc. to develop a practice management solution to meet their needs.[2] Enlisting the help of Todd's brother, software developer Ed Park, they developed a revenue cycle management system with a "rules engine" of dynamic billing rules data. The team quickly realized that their application could have broad appeal to other practices. In 2000, athenahealth introduced athenaCollector, its cloud-based revenue cycle and practice management service.[3]

Six years later, in 2006, the company launched athenaClinicals, touted as the "first economically sustainable, service-based" electronic medical records (EMR) system.[4] After years of rapid growth, athenahealth, Inc. announced an initial public offering of its common stock on June 22, 2007.[5] The offering was completed on September 20, 2007, at a price of $18 per share. It now trades on the NASDAQ exchange under the symbol ATHN.[6]

In 2008, athenahealth introduced athenaCommunicator to help ease practices’ phone call burden.[7] Since then, the product has evolved into a suite of "patient engagement services", including a patient portal[clarification needed], population health campaign tool, scheduling solution, and answering service. The company purchased Anodyne Health in 2009.[8] Its services were incorporated into athenaCoordinator Analytics, an analytics service for medical groups and health systems.

In 2011, athenahealth purchased Proxsys, LLC, a care coordination company, and launched athenaCoordinator (now athenaCoordinator Core) for order transmission and care collaboration with secure text message.[9] In 2012, it purchased Healthcare Data Services, an expert in population health management.[10] In an effort to create an end-to-end care coordination and population health service designed for enterprises, the company launched athenaCoordinator Enterprise in 2014.

In 2013, the company purchased the Epocrates mobile brand.[11] Epocrates is now an athenahealth service for clinical decision support in the moments of care.

On January 14, 2015, athenahealth announced the acquisition of RazorInsights, a leader in cloud-based EHR and financial solutions for rural, critical access, and community hospitals. The purchase extends athenahealth’s established position in the outpatient market into the 50-bed and under inpatient care environment, which accounts for nearly one third of the hospital market.[12] In February, 2015, athenahealth announced that it had purchased webOMR, the web-based clinical applications and EHR platform developed by Boston’s Beth Israel Deaconess Medical Center. athenahealth is collaborating with BIDMC on the development of athenahealth's acute care service offering, using Beth Israel Deaconess Hospital-Needham, a 58-bed community hospital, as the alpha development site.[13]